GenomeRNAi - a database for RNAi phenotypes and reagents

Phenotype information for gene 351 (APP)

Screen TitleGene IDGene SymbolReagent IDScorePhenotypeFollow Up
TRAIL-induced apoptosis (1)
NM_000484
APP
0.5
none yes

Reference

A synthetic lethal screen identifies FAT1 as an antagonist of caspase-8 in extrinsic apoptosis. Kranz and Boutros, 2014

The extrinsic apoptosis pathway is initiated by binding of death ligands to death receptors resulting in the formation of the death-inducing signaling complex (DISC). Activation of procaspase-8 within the DISC and its release from the signaling complex is required for processing executor caspases and commiting cell death. Here, we report that the atypical cadherin FAT1 interacts with caspase-8 preventing the association of caspase-8 with the DISC. We identified FAT1 in a genome-wide siRNA screen for synthetic lethal interactions with death receptor-mediated apoptosis. Knockdown of FAT1 sensitized established and patient-derived glioblastoma cell lines for apoptosis transduced by cell death ligands. Depletion of FAT1 resulted in enhanced procaspase-8 recruitment to the DISC and increased formation of caspase-8 containing secondary signaling complexes. In addition, FAT1 knockout cell lines generated by CRISPR/Cas9-mediated genome engineering were more susceptible for death receptor-mediated apoptosis. Our findings provide evidence for a mechanism to control caspase-8-dependent cell death by the atypical cadherin FAT1. These results contribute towards the understanding of effector caspase regulation in physiological conditions.

Screen Details

Stable ID: GR00240-S-1
Screen Title: TRAIL-induced apoptosis (1)
Assay: Viability
Method: Luminescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: U251MG
Library: Dharmacon, SMART-pool siRNA
Reagent Type: siRNA
Score Type: Z-score
Cutoff: > 4
Notes: Author-submitted data

Selective autophagy regulation (1)
NM_000484
APP
np
sp
none no

Reference

Image-based genome-wide siRNA screen identifies selective autophagy factors. Orvedahl et al., 2011

Selective autophagy involves the recognition and targeting of specific cargo, such as damaged organelles, misfolded proteins, or invading pathogens for lysosomal destruction. Yeast genetic screens have identified proteins required for different forms of selective autophagy, including cytoplasm-to-vacuole targeting, pexophagy and mitophagy, and mammalian genetic screens have identified proteins required for autophagy regulation. However, there have been no systematic approaches to identify molecular determinants of selective autophagy in mammalian cells. Here, to identify mammalian genes required for selective autophagy, we performed a high-content, image-based, genome-wide small interfering RNA screen to detect genes required for the colocalization of Sindbis virus capsid protein with autophagolysosomes. We identified 141 candidate genes required for viral autophagy, which were enriched for cellular pathways related to messenger RNA processing, interferon signalling, vesicle trafficking, cytoskeletal motor function and metabolism. Ninety-six of these genes were also required for Parkin-mediated mitophagy, indicating that common molecular determinants may be involved in autophagic targeting of viral nucleocapsids and autophagic targeting of damaged mitochondria. Murine embryonic fibroblasts lacking one of these gene products, the C2-domain containing protein, SMURF1, are deficient in the autophagosomal targeting of Sindbis and herpes simplex viruses and in the clearance of damaged mitochondria. Moreover, SMURF1-deficient mice accumulate damaged mitochondria in the heart, brain and liver. Thus, our study identifies candidate determinants of selective autophagy, and defines SMURF1 as a newly recognized mediator of both viral autophagy and mitophagy.

Screen Details

Stable ID: GR00242-A-1
Screen Title: Selective autophagy regulation (1)
Assay: Sindbis virus (SIN) capsid SIN-mCherry.capsid and autophagosome GFP–LC3 protein expression
Method: Fluorescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HeLa/GFP-LC3
Library: Dharmacon, siGenome
Reagent Type: siRNA
Score Type: Z-score
Cutoff: Complex criteria
Notes:

Genome stability
NM_000484
APP
np
sp
none no

Reference

A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability. Paulsen et al., 2009

Signaling pathways that respond to DNA damage are essential for the maintenance of genome stability and are linked to many diseases, including cancer. Here, a genome-wide siRNA screen was employed to identify additional genes involved in genome stabilization by monitoring phosphorylation of the histone variant H2AX, an early mark of DNA damage. We identified hundreds of genes whose downregulation led to elevated levels of H2AX phosphorylation (gammaH2AX) and revealed links to cellular complexes and to genes with unclassified functions. We demonstrate a widespread role for mRNA-processing factors in preventing DNA damage, which in some cases is caused by aberrant RNA-DNA structures. Furthermore, we connect increased gammaH2AX levels to the neurological disorder Charcot-Marie-Tooth (CMT) syndrome, and we find a role for several CMT proteins in the DNA-damage response. These data indicate that preservation of genome stability is mediated by a larger network of biological processes than previously appreciated.

Screen Details

Stable ID: GR00053-A
Screen Title: Genome stability
Assay: gamma-H2AX phosphorylation and DNA content
Method: Fluorescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HeLa
Library: ThermoFisher Scientific, siARRAY human genome siRNA library
Reagent Type: siRNA
Score Type: p-value
Cutoff: Complex criteria
Notes: Confidence groupings from 4 to 1 (highest level of confidence in group 4)

Ciliogenesis and cilium length (1)
351
APP
114057
-39.24
none no

Reference

Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al., 2010

Primary cilia are evolutionarily conserved cellular organelles that organize diverse signalling pathways. Defects in the formation or function of primary cilia are associated with a spectrum of human diseases and developmental abnormalities. Genetic screens in model organisms have discovered core machineries of cilium assembly and maintenance. However, regulatory molecules that coordinate the biogenesis of primary cilia with other cellular processes, including cytoskeletal organization, vesicle trafficking and cell-cell adhesion, remain to be identified. Here we report the results of a functional genomic screen using RNA interference (RNAi) to identify human genes involved in ciliogenesis control. The screen identified 36 positive and 13 negative ciliogenesis modulators, which include molecules involved in actin dynamics and vesicle trafficking. Further investigation demonstrated that blocking actin assembly facilitates ciliogenesis by stabilizing the pericentrosomal preciliary compartment (PPC), a previously uncharacterized compact vesiculotubular structure storing transmembrane proteins destined for cilia during the early phase of ciliogenesis. The PPC was labelled by recycling endosome markers. Moreover, knockdown of modulators that are involved in the endocytic recycling pathway affected the formation of the PPC as well as ciliogenesis. Our results uncover a critical regulatory step that couples actin dynamics and endocytic recycling with ciliogenesis, and also provides potential target molecules for future study.

Screen Details

Stable ID: GR00149-A-1
Screen Title: Ciliogenesis and cilium length (1)
Assay: Smoothed protein expression
Method: Fluorescence
Scope: Druggable genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: htRPE
Library: Ambion, Human druggable genome siRNA library V3.1
Reagent Type: siRNA
Score Type: Normalized percent inhibition
Cutoff: > 1.5 OR < -1.5 standard deviations from mean
Notes:

Ciliogenesis and cilium length (1)
351
APP
2530
-13.55
none no

Reference

Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al., 2010

Primary cilia are evolutionarily conserved cellular organelles that organize diverse signalling pathways. Defects in the formation or function of primary cilia are associated with a spectrum of human diseases and developmental abnormalities. Genetic screens in model organisms have discovered core machineries of cilium assembly and maintenance. However, regulatory molecules that coordinate the biogenesis of primary cilia with other cellular processes, including cytoskeletal organization, vesicle trafficking and cell-cell adhesion, remain to be identified. Here we report the results of a functional genomic screen using RNA interference (RNAi) to identify human genes involved in ciliogenesis control. The screen identified 36 positive and 13 negative ciliogenesis modulators, which include molecules involved in actin dynamics and vesicle trafficking. Further investigation demonstrated that blocking actin assembly facilitates ciliogenesis by stabilizing the pericentrosomal preciliary compartment (PPC), a previously uncharacterized compact vesiculotubular structure storing transmembrane proteins destined for cilia during the early phase of ciliogenesis. The PPC was labelled by recycling endosome markers. Moreover, knockdown of modulators that are involved in the endocytic recycling pathway affected the formation of the PPC as well as ciliogenesis. Our results uncover a critical regulatory step that couples actin dynamics and endocytic recycling with ciliogenesis, and also provides potential target molecules for future study.

Screen Details

Stable ID: GR00149-A-1
Screen Title: Ciliogenesis and cilium length (1)
Assay: Smoothed protein expression
Method: Fluorescence
Scope: Druggable genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: htRPE
Library: Ambion, Human druggable genome siRNA library V3.1
Reagent Type: siRNA
Score Type: Normalized percent inhibition
Cutoff: > 1.5 OR < -1.5 standard deviations from mean
Notes:

Melanogenesis
NM_000484
APP
np
0.91
none no

Reference

Genome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells. Ganesan et al., 2008

Melanin protects the skin and eyes from the harmful effects of UV irradiation, protects neural cells from toxic insults, and is required for sound conduction in the inner ear. Aberrant regulation of melanogenesis underlies skin disorders (melasma and vitiligo), neurologic disorders (Parkinson''s disease), auditory disorders (Waardenburg''s syndrome), and opthalmologic disorders (age related macular degeneration). Much of the core synthetic machinery driving melanin production has been identified; however, the spectrum of gene products participating in melanogenesis in different physiological niches is poorly understood. Functional genomics based on RNA-mediated interference (RNAi) provides the opportunity to derive unbiased comprehensive collections of pharmaceutically tractable single gene targets supporting melanin production. In this study, we have combined a high-throughput, cell-based, one-well/one-gene screening platform with a genome-wide arrayed synthetic library of chemically synthesized, small interfering RNAs to identify novel biological pathways that govern melanin biogenesis in human melanocytes. Ninety-two novel genes that support pigment production were identified with a low false discovery rate. Secondary validation and preliminary mechanistic studies identified a large panel of targets that converge on tyrosinase expression and stability. Small molecule inhibition of a family of gene products in this class was sufficient to impair chronic tyrosinase expression in pigmented melanoma cells and UV-induced tyrosinase expression in primary melanocytes. Isolation of molecular machinery known to support autophagosome biosynthesis from this screen, together with in vitro and in vivo validation, exposed a close functional relationship between melanogenesis and autophagy. In summary, these studies illustrate the power of RNAi-based functional genomics to identify novel genes, pathways, and pharmacologic agents that impact a biological phenotype and operate outside of preconceived mechanistic relationships.

Screen Details

Stable ID: GR00056-A
Screen Title: Melanogenesis
Assay: Melanin protein expression and viability
Method: Absorbance and luminescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: MNT-1
Library: Dharmacon, rp
Reagent Type: siRNA
Score Type: Normalized absorbance ratio
Cutoff: > 2 standard deviations below mean
Notes: Additional information about a secondary screen (retest to determine false-positive rate)

Ciliogenesis and cilium length (1)
351
APP
118200
3.38
none no

Reference

Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al., 2010

Primary cilia are evolutionarily conserved cellular organelles that organize diverse signalling pathways. Defects in the formation or function of primary cilia are associated with a spectrum of human diseases and developmental abnormalities. Genetic screens in model organisms have discovered core machineries of cilium assembly and maintenance. However, regulatory molecules that coordinate the biogenesis of primary cilia with other cellular processes, including cytoskeletal organization, vesicle trafficking and cell-cell adhesion, remain to be identified. Here we report the results of a functional genomic screen using RNA interference (RNAi) to identify human genes involved in ciliogenesis control. The screen identified 36 positive and 13 negative ciliogenesis modulators, which include molecules involved in actin dynamics and vesicle trafficking. Further investigation demonstrated that blocking actin assembly facilitates ciliogenesis by stabilizing the pericentrosomal preciliary compartment (PPC), a previously uncharacterized compact vesiculotubular structure storing transmembrane proteins destined for cilia during the early phase of ciliogenesis. The PPC was labelled by recycling endosome markers. Moreover, knockdown of modulators that are involved in the endocytic recycling pathway affected the formation of the PPC as well as ciliogenesis. Our results uncover a critical regulatory step that couples actin dynamics and endocytic recycling with ciliogenesis, and also provides potential target molecules for future study.

Screen Details

Stable ID: GR00149-A-1
Screen Title: Ciliogenesis and cilium length (1)
Assay: Smoothed protein expression
Method: Fluorescence
Scope: Druggable genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: htRPE
Library: Ambion, Human druggable genome siRNA library V3.1
Reagent Type: siRNA
Score Type: Normalized percent inhibition
Cutoff: > 1.5 OR < -1.5 standard deviations from mean
Notes:

Homologous recombination DNA double-strand break repair (HR-DSBR) (1)
ENSG00000142192
APP
np
0.37
none no

Reference

A genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia. Słabicki et al., 2010

DNA repair is essential to maintain genome integrity, and genes with roles in DNA repair are frequently mutated in a variety of human diseases. Repair via homologous recombination typically restores the original DNA sequence without introducing mutations, and a number of genes that are required for homologous recombination DNA double-strand break repair (HR-DSBR) have been identified. However, a systematic analysis of this important DNA repair pathway in mammalian cells has not been reported. Here, we describe a genome-scale endoribonuclease-prepared short interfering RNA (esiRNA) screen for genes involved in DNA double strand break repair. We report 61 genes that influenced the frequency of HR-DSBR and characterize in detail one of the genes that decreased the frequency of HR-DSBR. We show that the gene KIAA0415 encodes a putative helicase that interacts with SPG11 and SPG15, two proteins mutated in hereditary spastic paraplegia (HSP). We identify mutations in HSP patients, discovering KIAA0415/SPG48 as a novel HSP-associated gene, and show that a KIAA0415/SPG48 mutant cell line is more sensitive to DNA damaging drugs. We present the first genome-scale survey of HR-DSBR in mammalian cells providing a dataset that should accelerate the discovery of novel genes with roles in DNA repair and associated medical conditions. The discovery that proteins forming a novel protein complex are required for efficient HR-DSBR and are mutated in patients suffering from HSP suggests a link between HSP and DNA repair.

Screen Details

Stable ID: GR00151-A-1
Screen Title: Homologous recombination DNA double-strand break repair (HR-DSBR) (1)
Assay: (HR-DSBR) DR-GFP reporter
Method: Flow cytometry
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HeLa
Library: Custom-made, Custom-made
Reagent Type: esiRNA
Score Type: Z-score
Cutoff: < -2 OR > 2
Notes:

TRAIL-induced apoptosis (2)
NM_000484
APP
3.77
Decreased viability with TRAIL no

Reference

A synthetic lethal screen identifies FAT1 as an antagonist of caspase-8 in extrinsic apoptosis. Kranz and Boutros, 2014

The extrinsic apoptosis pathway is initiated by binding of death ligands to death receptors resulting in the formation of the death-inducing signaling complex (DISC). Activation of procaspase-8 within the DISC and its release from the signaling complex is required for processing executor caspases and commiting cell death. Here, we report that the atypical cadherin FAT1 interacts with caspase-8 preventing the association of caspase-8 with the DISC. We identified FAT1 in a genome-wide siRNA screen for synthetic lethal interactions with death receptor-mediated apoptosis. Knockdown of FAT1 sensitized established and patient-derived glioblastoma cell lines for apoptosis transduced by cell death ligands. Depletion of FAT1 resulted in enhanced procaspase-8 recruitment to the DISC and increased formation of caspase-8 containing secondary signaling complexes. In addition, FAT1 knockout cell lines generated by CRISPR/Cas9-mediated genome engineering were more susceptible for death receptor-mediated apoptosis. Our findings provide evidence for a mechanism to control caspase-8-dependent cell death by the atypical cadherin FAT1. These results contribute towards the understanding of effector caspase regulation in physiological conditions.

Screen Details

Stable ID: GR00240-S-2
Screen Title: TRAIL-induced apoptosis (2)
Assay: Viability (synthetic lethal)
Method: Luminescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: U251MG
Library: Dharmacon, SMART-pool siRNA
Reagent Type: siRNA
Score Type: Differential score
Cutoff: > 3.6 AND viability Z-score < 4
Notes: Author-submitted data. Z-scores from viability screen (1) are considered in score interpretation for this screen. Additional comments are available via the download function

Ciliogenesis and cilium length (1)
351
APP
114057
-22.12
none no

Reference

Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al., 2010

Primary cilia are evolutionarily conserved cellular organelles that organize diverse signalling pathways. Defects in the formation or function of primary cilia are associated with a spectrum of human diseases and developmental abnormalities. Genetic screens in model organisms have discovered core machineries of cilium assembly and maintenance. However, regulatory molecules that coordinate the biogenesis of primary cilia with other cellular processes, including cytoskeletal organization, vesicle trafficking and cell-cell adhesion, remain to be identified. Here we report the results of a functional genomic screen using RNA interference (RNAi) to identify human genes involved in ciliogenesis control. The screen identified 36 positive and 13 negative ciliogenesis modulators, which include molecules involved in actin dynamics and vesicle trafficking. Further investigation demonstrated that blocking actin assembly facilitates ciliogenesis by stabilizing the pericentrosomal preciliary compartment (PPC), a previously uncharacterized compact vesiculotubular structure storing transmembrane proteins destined for cilia during the early phase of ciliogenesis. The PPC was labelled by recycling endosome markers. Moreover, knockdown of modulators that are involved in the endocytic recycling pathway affected the formation of the PPC as well as ciliogenesis. Our results uncover a critical regulatory step that couples actin dynamics and endocytic recycling with ciliogenesis, and also provides potential target molecules for future study.

Screen Details

Stable ID: GR00149-A-1
Screen Title: Ciliogenesis and cilium length (1)
Assay: Smoothed protein expression
Method: Fluorescence
Scope: Druggable genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: htRPE
Library: Ambion, Human druggable genome siRNA library V3.1
Reagent Type: siRNA
Score Type: Normalized percent inhibition
Cutoff: > 1.5 OR < -1.5 standard deviations from mean
Notes:

Ciliogenesis and cilium length (1)
351
APP
2530
-54.74
none no

Reference

Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al., 2010

Primary cilia are evolutionarily conserved cellular organelles that organize diverse signalling pathways. Defects in the formation or function of primary cilia are associated with a spectrum of human diseases and developmental abnormalities. Genetic screens in model organisms have discovered core machineries of cilium assembly and maintenance. However, regulatory molecules that coordinate the biogenesis of primary cilia with other cellular processes, including cytoskeletal organization, vesicle trafficking and cell-cell adhesion, remain to be identified. Here we report the results of a functional genomic screen using RNA interference (RNAi) to identify human genes involved in ciliogenesis control. The screen identified 36 positive and 13 negative ciliogenesis modulators, which include molecules involved in actin dynamics and vesicle trafficking. Further investigation demonstrated that blocking actin assembly facilitates ciliogenesis by stabilizing the pericentrosomal preciliary compartment (PPC), a previously uncharacterized compact vesiculotubular structure storing transmembrane proteins destined for cilia during the early phase of ciliogenesis. The PPC was labelled by recycling endosome markers. Moreover, knockdown of modulators that are involved in the endocytic recycling pathway affected the formation of the PPC as well as ciliogenesis. Our results uncover a critical regulatory step that couples actin dynamics and endocytic recycling with ciliogenesis, and also provides potential target molecules for future study.

Screen Details

Stable ID: GR00149-A-1
Screen Title: Ciliogenesis and cilium length (1)
Assay: Smoothed protein expression
Method: Fluorescence
Scope: Druggable genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: htRPE
Library: Ambion, Human druggable genome siRNA library V3.1
Reagent Type: siRNA
Score Type: Normalized percent inhibition
Cutoff: > 1.5 OR < -1.5 standard deviations from mean
Notes:

Wnt/beta-catenin pathway regulation
351
APP
np
3.13
Upregulation of Wnt/beta-catenin pathway after WNT3A stimulation no

Reference

Bruton's tyrosine kinase revealed as a negative regulator of Wnt-beta-catenin signaling. James et al., 2009

Wnts are secreted ligands that activate several receptor-mediated signal transduction cascades. Homeostatic Wnt signaling through beta-catenin is required in adults, because either elevation or attenuation of beta-catenin function has been linked to diverse diseases. To contribute to the identification of both protein and pharmacological regulators of this pathway, we describe a combinatorial screen that merged data from a high-throughput screen of known bioactive compounds with an independent focused small interfering RNA screen. Each screen independently revealed Bruton''s tyrosine kinase (BTK) as an inhibitor of Wnt-beta-catenin signaling. Loss of BTK function in human colorectal cancer cells, human B cells, zebrafish embryos, and cells derived from X-linked agammaglobulinemia patients with a mutant BTK gene resulted in elevated Wnt-beta-catenin signaling, confirming that BTK acts as a negative regulator of this pathway. From affinity purification-mass spectrometry and biochemical binding studies, we found that BTK directly interacts with a nuclear component of Wnt-beta-catenin signaling, CDC73. Further, we show that BTK increased the abundance of CDC73 in the absence of stimulation and that CDC73 acted as a repressor of beta-catenin-mediated transcription in human colorectal cancer cells and B cells.

Screen Details

Stable ID: GR00016-A
Screen Title: Wnt/beta-catenin pathway regulation
Assay: Wnt/beta-catenin pathway reporter
Method: Luminescence
Scope: Selected genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: RKO
Library: rp, rp
Reagent Type: siRNA
Score Type: Z-score
Cutoff: > 2
Notes:

Ciliogenesis and cilium length (1)
351
APP
118200
36.36
none no

Reference

Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al., 2010

Primary cilia are evolutionarily conserved cellular organelles that organize diverse signalling pathways. Defects in the formation or function of primary cilia are associated with a spectrum of human diseases and developmental abnormalities. Genetic screens in model organisms have discovered core machineries of cilium assembly and maintenance. However, regulatory molecules that coordinate the biogenesis of primary cilia with other cellular processes, including cytoskeletal organization, vesicle trafficking and cell-cell adhesion, remain to be identified. Here we report the results of a functional genomic screen using RNA interference (RNAi) to identify human genes involved in ciliogenesis control. The screen identified 36 positive and 13 negative ciliogenesis modulators, which include molecules involved in actin dynamics and vesicle trafficking. Further investigation demonstrated that blocking actin assembly facilitates ciliogenesis by stabilizing the pericentrosomal preciliary compartment (PPC), a previously uncharacterized compact vesiculotubular structure storing transmembrane proteins destined for cilia during the early phase of ciliogenesis. The PPC was labelled by recycling endosome markers. Moreover, knockdown of modulators that are involved in the endocytic recycling pathway affected the formation of the PPC as well as ciliogenesis. Our results uncover a critical regulatory step that couples actin dynamics and endocytic recycling with ciliogenesis, and also provides potential target molecules for future study.

Screen Details

Stable ID: GR00149-A-1
Screen Title: Ciliogenesis and cilium length (1)
Assay: Smoothed protein expression
Method: Fluorescence
Scope: Druggable genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: htRPE
Library: Ambion, Human druggable genome siRNA library V3.1
Reagent Type: siRNA
Score Type: Normalized percent inhibition
Cutoff: > 1.5 OR < -1.5 standard deviations from mean
Notes:

Combinatorial effect with paclitaxel
NM_000484
APP
np
1.13
none no

Reference

Synthetic lethal screen identification of chemosensitizer loci in cancer cells. Whitehurst et al., 2007

Abundant evidence suggests that a unifying principle governing the molecular pathology of cancer is the co-dependent aberrant regulation of core machinery driving proliferation and suppressing apoptosis. Anomalous proteins engaged in support of this tumorigenic regulatory environment most probably represent optimal intervention targets in a heterogeneous population of cancer cells. The advent of RNA-mediated interference (RNAi)-based functional genomics provides the opportunity to derive unbiased comprehensive collections of validated gene targets supporting critical biological systems outside the framework of preconceived notions of mechanistic relationships. We have combined a high-throughput cell-based one-well/one-gene screening platform with a genome-wide synthetic library of chemically synthesized small interfering RNAs for systematic interrogation of the molecular underpinnings of cancer cell chemoresponsiveness. NCI-H1155, a human non-small-cell lung cancer line, was employed in a paclitaxel-dependent synthetic lethal screen designed to identify gene targets that specifically reduce cell viability in the presence of otherwise sublethal concentrations of paclitaxel. Using a stringent objective statistical algorithm to reduce false discovery rates below 5%, we isolated a panel of 87 genes that represent major focal points of the autonomous response of cancer cells to the abrogation of microtubule dynamics. Here we show that several of these targets sensitize lung cancer cells to paclitaxel concentrations 1,000-fold lower than otherwise required for a significant response, and we identify mechanistic relationships between cancer-associated aberrant gene expression programmes and the basic cellular machinery required for robust mitotic progression.

Screen Details

Stable ID: GR00054-A
Screen Title: Combinatorial effect with paclitaxel
Assay: Viability (synthetic lethal)
Method: ATP level
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: NCI-H1155
Library: Dharmacon, # G-005000-01
Reagent Type: siRNA
Score Type: Paclitaxel/control ratio
Cutoff: Complex criteria
Notes: Additional information about 87 high-confidence hits

TP53 interactions (1)
ENSG00000142192
np
sp
none no

Reference

A systematic RNAi synthetic interaction screen reveals a link between p53 and snoRNP assembly. Krastev et al., 2011

TP53 (tumour protein 53) is one of the most frequently mutated genes in human cancer and its role during cellular transformation has been studied extensively. However, the homeostatic functions of p53 are less well understood. Here, we explore the molecular dependency network of TP53 through an RNAi-mediated synthetic interaction screen employing two HCT116 isogenic cell lines and a genome-scale endoribonuclease-prepared short interfering RNA library. We identify a variety of TP53 synthetic interactions unmasking the complex connections of p53 to cellular physiology and growth control. Molecular dissection of the TP53 synthetic interaction with UNRIP indicates an enhanced dependency of TP53-negative cells on small nucleolar ribonucleoprotein (snoRNP) assembly. This dependency is mediated by the snoRNP chaperone gene NOLC1 (also known as NOPP140), which we identify as a physiological p53 target gene. This unanticipated function of TP53 in snoRNP assembly highlights the potential of RNAi-mediated synthetic interaction screens to dissect molecular pathways of tumour suppressor genes.

Screen Details

Stable ID: GR00196-A-1
Screen Title: TP53 interactions (1)
Assay: TP53 protein expression and viability
Method: Fluorescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HCT116 ( wildtype and TP53 knockout)
Library: Custom-made, rp
Reagent Type: esiRNA
Score Type: Complex, sp
Cutoff: Complex criteria
Notes:

Salmonella enterica subspecies 1 serovar Typhimurium invasion (1)
351
APP
np
0.4
none no

Reference

RNAi screen of Salmonella invasion shows role of COPI in membrane targeting of cholesterol and Cdc42. Misselwitz et al., 2011

The pathogen Salmonella Typhimurium is a common cause of diarrhea and invades the gut tissue by injecting a cocktail of virulence factors into epithelial cells, triggering actin rearrangements, membrane ruffling and pathogen entry. One of these factors is SopE, a G-nucleotide exchange factor for the host cellular Rho GTPases Rac1 and Cdc42. How SopE mediates cellular invasion is incompletely understood. Using genome-scale RNAi screening we identified 72 known and novel host cell proteins affecting SopE-mediated entry. Follow-up assays assigned these ''hits'' to particular steps of the invasion process; i.e., binding, effector injection, membrane ruffling, membrane closure and maturation of the Salmonella-containing vacuole. Depletion of the COPI complex revealed a unique effect on virulence factor injection and membrane ruffling. Both effects are attributable to mislocalization of cholesterol, sphingolipids, Rac1 and Cdc42 away from the plasma membrane into a large intracellular compartment. Equivalent results were obtained with the vesicular stomatitis virus. Therefore, COPI-facilitated maintenance of lipids may represent a novel, unifying mechanism essential for a wide range of pathogens, offering opportunities for designing new drugs.

Screen Details

Stable ID: GR00133-A-1
Screen Title: Salmonella enterica subspecies 1 serovar Typhimurium invasion (1)
Assay: Gentamycin protection invasion assay
Method: Fluorescence
Scope: Druggable genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HeLa
Library: Qiagen, Druggable genome library V2.0
Reagent Type: siRNA
Score Type: log2 median
Cutoff: Complex criteria
Notes:

Self-renewal and pluripotency in human embryonic stem cells (1)
NM_000484
APP
-1.17
none no

Reference

A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al., 2010

The derivation of human ES cells (hESCs) from human blastocysts represents one of the milestones in stem cell biology. The full potential of hESCs in research and clinical applications requires a detailed understanding of the genetic network that governs the unique properties of hESCs. Here, we report a genome-wide RNA interference screen to identify genes which regulate self-renewal and pluripotency properties in hESCs. Interestingly, functionally distinct complexes involved in transcriptional regulation and chromatin remodelling are among the factors identified in the screen. To understand the roles of these potential regulators of hESCs, we studied transcription factor PRDM14 to gain new insights into its functional roles in the regulation of pluripotency. We showed that PRDM14 regulates directly the expression of key pluripotency gene POU5F1 through its proximal enhancer. Genome-wide location profiling experiments revealed that PRDM14 colocalized extensively with other key transcription factors such as OCT4, NANOG and SOX2, indicating that PRDM14 is integrated into the core transcriptional regulatory network. More importantly, in a gain-of-function assay, we showed that PRDM14 is able to enhance the efficiency of reprogramming of human fibroblasts in conjunction with OCT4, SOX2 and KLF4. Altogether, our study uncovers a wealth of novel hESC regulators wherein PRDM14 exemplifies a key transcription factor required for the maintenance of hESC identity and the reacquisition of pluripotency in human somatic cells.

Screen Details

Stable ID: GR00184-A-1
Screen Title: Self-renewal and pluripotency in human embryonic stem cells (1)
Assay: POU5F1 protein expression
Method: Fluorescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: hESC H1
Library: Dharmacon, SMARTpool siRNA library
Reagent Type: siRNA
Score Type: Z-score
Cutoff: < -2
Notes:

Homologous recombination DNA double-strand break repair (HR-DSBR) (1)
351
APP
0.53
none no

Reference

A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response. Adamson et al., 2012

Repair of DNA double-strand breaks is critical to genomic stability and the prevention of developmental disorders and cancer. A central pathway for this repair is homologous recombination (HR). Most knowledge of HR is derived from work in prokaryotic and eukaryotic model organisms. We carried out a genome-wide siRNA-based screen in human cells. Among positive regulators of HR we identified networks of DNA-damage-response and pre-mRNA-processing proteins, and among negative regulators we identified a phosphatase network. Three candidate proteins localized to DNA lesions, including RBMX, a heterogeneous nuclear ribonucleoprotein that has a role in alternative splicing. RBMX accumulated at DNA lesions through multiple domains in a poly(ADP-ribose) polymerase 1-dependent manner and promoted HR by facilitating proper BRCA2 expression. Our screen also revealed that off-target depletion of RAD51 is a common source of RNAi false positives, raising a cautionary note for siRNA screens and RNAi-based studies of HR.

Screen Details

Stable ID: GR00236-A-1
Screen Title: Homologous recombination DNA double-strand break repair (HR-DSBR) (1)
Assay: (HR-DSBR) DR-GFP reporter and DNA content
Method: Fluorescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: DR-U2OS
Library: Dharmacon, Human siGENOME siRNA (G-005000-05)
Reagent Type: siRNA
Score Type: Relative HR ratio
Cutoff: < ~0.4 OR > 1.88
Notes: Cutoff values correspond 2 standard deviations from the screen-wide mean

Hepatitis C virus replication (1)
351
APP
PL-50008
0.92
none no

Reference

A functional genomic screen identifies cellular cofactors of hepatitis C virus replication. Tai et al., 2009

Hepatitis C virus (HCV) chronically infects 3% of the world''s population, and complications from HCV are the leading indication for liver transplantation. Given the need for better anti-HCV therapies, one strategy is to identify and target cellular cofactors of the virus lifecycle. Using a genome-wide siRNA library, we identified 96 human genes that support HCV replication, with a significant number of them being involved in vesicle organization and biogenesis. Phosphatidylinositol 4-kinase PI4KA and multiple subunits of the COPI vesicle coat complex were among the genes identified. Consistent with this, pharmacologic inhibitors of COPI and PI4KA blocked HCV replication. Targeting hepcidin, a peptide critical for iron homeostasis, also affected HCV replication, which may explain the known dysregulation of iron homeostasis in HCV infection. The host cofactors for HCV replication identified in this study should serve as a useful resource in delineating new targets for anti-HCV therapies.

Screen Details

Stable ID: GR00180-A-1
Screen Title: Hepatitis C virus replication (1)
Assay: HCV replicon RNA copy number
Method: Luminescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: Huh7/Rep-Feo
Library: Dharmacon, siARRAY Human Genome siRNA Library
Reagent Type: siRNA
Score Type: q-value
Cutoff: Complex criteria
Notes:

Ciliogenesis and cilium length (1)
351
APP
114058
-97.5
none no

Reference

Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al., 2010

Primary cilia are evolutionarily conserved cellular organelles that organize diverse signalling pathways. Defects in the formation or function of primary cilia are associated with a spectrum of human diseases and developmental abnormalities. Genetic screens in model organisms have discovered core machineries of cilium assembly and maintenance. However, regulatory molecules that coordinate the biogenesis of primary cilia with other cellular processes, including cytoskeletal organization, vesicle trafficking and cell-cell adhesion, remain to be identified. Here we report the results of a functional genomic screen using RNA interference (RNAi) to identify human genes involved in ciliogenesis control. The screen identified 36 positive and 13 negative ciliogenesis modulators, which include molecules involved in actin dynamics and vesicle trafficking. Further investigation demonstrated that blocking actin assembly facilitates ciliogenesis by stabilizing the pericentrosomal preciliary compartment (PPC), a previously uncharacterized compact vesiculotubular structure storing transmembrane proteins destined for cilia during the early phase of ciliogenesis. The PPC was labelled by recycling endosome markers. Moreover, knockdown of modulators that are involved in the endocytic recycling pathway affected the formation of the PPC as well as ciliogenesis. Our results uncover a critical regulatory step that couples actin dynamics and endocytic recycling with ciliogenesis, and also provides potential target molecules for future study.

Screen Details

Stable ID: GR00149-A-1
Screen Title: Ciliogenesis and cilium length (1)
Assay: Smoothed protein expression
Method: Fluorescence
Scope: Druggable genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: htRPE
Library: Ambion, Human druggable genome siRNA library V3.1
Reagent Type: siRNA
Score Type: Normalized percent inhibition
Cutoff: > 1.5 OR < -1.5 standard deviations from mean
Notes:

Ciliogenesis and cilium length (1)
351
APP
114058
-131.65
none no

Reference

Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al., 2010

Primary cilia are evolutionarily conserved cellular organelles that organize diverse signalling pathways. Defects in the formation or function of primary cilia are associated with a spectrum of human diseases and developmental abnormalities. Genetic screens in model organisms have discovered core machineries of cilium assembly and maintenance. However, regulatory molecules that coordinate the biogenesis of primary cilia with other cellular processes, including cytoskeletal organization, vesicle trafficking and cell-cell adhesion, remain to be identified. Here we report the results of a functional genomic screen using RNA interference (RNAi) to identify human genes involved in ciliogenesis control. The screen identified 36 positive and 13 negative ciliogenesis modulators, which include molecules involved in actin dynamics and vesicle trafficking. Further investigation demonstrated that blocking actin assembly facilitates ciliogenesis by stabilizing the pericentrosomal preciliary compartment (PPC), a previously uncharacterized compact vesiculotubular structure storing transmembrane proteins destined for cilia during the early phase of ciliogenesis. The PPC was labelled by recycling endosome markers. Moreover, knockdown of modulators that are involved in the endocytic recycling pathway affected the formation of the PPC as well as ciliogenesis. Our results uncover a critical regulatory step that couples actin dynamics and endocytic recycling with ciliogenesis, and also provides potential target molecules for future study.

Screen Details

Stable ID: GR00149-A-1
Screen Title: Ciliogenesis and cilium length (1)
Assay: Smoothed protein expression
Method: Fluorescence
Scope: Druggable genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: htRPE
Library: Ambion, Human druggable genome siRNA library V3.1
Reagent Type: siRNA
Score Type: Normalized percent inhibition
Cutoff: > 1.5 OR < -1.5 standard deviations from mean
Notes:

Human papillomavirus oncogene expression regulation (1)
351
APP
-0.07
none no

Reference

Genome-wide siRNA screen identifies SMCX, EP400, and Brd4 as E2-dependent regulators of human papillomavirus oncogene expression. Smith et al., 2010

An essential step in the pathogenesis of human papillomavirus (HPV)-associated cancers is the dysregulated expression of the viral oncogenes. The papillomavirus E2 protein can silence the long control region (LCR) promoter that controls viral E6 and E7 oncogene expression. The mechanisms by which E2 represses oncogene expression and the cellular factors through which E2 mediates this silencing are largely unknown. We conducted an unbiased, genome-wide siRNA screen and series of secondary screens that identified 96 cellular genes that contribute to the repression of the HPV LCR. In addition to confirming a role for the E2-binding bromodomain protein Brd4 in E2-mediated silencing, we identified a number of genes that have not previously been implicated in E2 repression, including the demethylase JARID1C/SMCX as well as EP400, a component of the NuA4/TIP60 histone acetyltransferase complex. Each of these genes contributes independently and additively to E2-mediated silencing, indicating that E2 functions through several distinct cellular complexes to repress E6 and E7 expression.

Screen Details

Stable ID: GR00197-A-1
Screen Title: Human papillomavirus oncogene expression regulation (1)
Assay: HPV18 LCR reporter activity
Method: Luminescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: C33A/BE2/18LCR c4
Library: Dharmacon, Human siGENOME SMARTpool library
Reagent Type: siRNA
Score Type: Z-score
Cutoff: >= 2
Notes: Author-submitted data. Phenotype strength according to Z-scores: weak: 2 - 3; moderate: 3 - 5; strong: > 5

Cell division (1)
ENSG00000142192
APP
ENSG00000142192
sp
none no

Reference

Genome-scale RNAi profiling of cell division in human tissue culture cells. Kittler et al., 2007

Cell division is fundamental for all organisms. Here we report a genome-scale RNA-mediated interference screen in HeLa cells designed to identify human genes that are important for cell division. We have used a library of endoribonuclease-prepared short interfering RNAs for gene silencing and have used DNA content analysis to identify genes that induced cell cycle arrest or altered ploidy on silencing. Validation and secondary assays were performed to generate a nine-parameter loss-of-function phenoprint for each of the genes. These phenotypic signatures allowed the assignment of genes to specific functional classes by combining hierarchical clustering, cross-species analysis and proteomic data mining. We highlight the richness of our dataset by ascribing novel functions to genes in mitosis and cytokinesis. In particular, we identify two evolutionarily conserved transcriptional regulatory networks that govern cytokinesis. Our work provides an experimental framework from which the systematic analysis of novel genes necessary for cell division in human cells can begin.

Screen Details

Stable ID: GR00098-A-1
Screen Title: Cell division (1)
Assay: Cell number and DNA content
Method: Laser scanning cytometry
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HeLa
Library: Custom-made, rp
Reagent Type: esiRNA
Score Type: Complex, sp
Cutoff: Complex criteria
Notes:

Reagent information for gene 351 (APP)

Reagent IDTypeLibrary
D-003731-04 siRNA
siGENOME|Thermo Scientific Dharmacon|1|RefSeq release 5-7|84206 siRNAs in pools of four|siRNA|http://www.dharmacon.com/
D-003731-01 siRNA
siGENOME|Thermo Scientific Dharmacon|1|RefSeq release 5-7|84206 siRNAs in pools of four|siRNA|http://www.dharmacon.com/
D-003731-02 siRNA
siGENOME|Thermo Scientific Dharmacon|1|RefSeq release 5-7|84206 siRNAs in pools of four|siRNA|http://www.dharmacon.com/
D-003731-03 siRNA
siGENOME|Thermo Scientific Dharmacon|1|RefSeq release 5-7|84206 siRNAs in pools of four|siRNA|http://www.dharmacon.com/
M-003731-00 siRNA_Pool
siGENOME|Thermo Scientific Dharmacon|1|RefSeq release 5-7|84206 siRNAs in pools of four|siRNA|http://www.dharmacon.com/
SP00003391 siRNA_Pool
Druggable and whole genome supplement|Qiagen|1, 3|RefSeq|70308 siRNAs in pools of four|siRNA|http://www.qiagen.com/
SI02623586 siRNA
Druggable and whole genome supplement|Qiagen|1, 3|RefSeq|70308 siRNAs in pools of four|siRNA|http://www.qiagen.com/
SI02776893 siRNA
Druggable and whole genome supplement|Qiagen|1, 3|RefSeq|70308 siRNAs in pools of four|siRNA|http://www.qiagen.com/
SI02780281 siRNA
Druggable and whole genome supplement|Qiagen|1, 3|RefSeq|70308 siRNAs in pools of four|siRNA|http://www.qiagen.com/
SI02780288 siRNA
Druggable and whole genome supplement|Qiagen|1, 3|RefSeq|70308 siRNAs in pools of four|siRNA|http://www.qiagen.com/
TRCN0000006705 shRNA
TRC shRNA Library|The RNAi Consortium (TRC)|1|RefSeq|81054|shRNA|http://www.broadinstitute.org/rnai/public/
TRCN0000011043 shRNA
TRC shRNA Library|The RNAi Consortium (TRC)|1|RefSeq|81054|shRNA|http://www.broadinstitute.org/rnai/public/
TRCN0000006706 shRNA
TRC shRNA Library|The RNAi Consortium (TRC)|1|RefSeq|81054|shRNA|http://www.broadinstitute.org/rnai/public/
TRCN0000006707 shRNA
TRC shRNA Library|The RNAi Consortium (TRC)|1|RefSeq|81054|shRNA|http://www.broadinstitute.org/rnai/public/
TRCN0000011042 shRNA
TRC shRNA Library|The RNAi Consortium (TRC)|1|RefSeq|81054|shRNA|http://www.broadinstitute.org/rnai/public/
s1502 siRNA
Ambion Silencer Select|Ambion|1|RefSeq|64781|siRNA|http://www.invitrogen.com/site/us/en/home/brands/ambion.html?CID=fl-ambion
s1501 siRNA
Ambion Silencer Select|Ambion|1|RefSeq|64781|siRNA|http://www.invitrogen.com/site/us/en/home/brands/ambion.html?CID=fl-ambion
s1500 siRNA
Ambion Silencer Select|Ambion|1|RefSeq|64781|siRNA|http://www.invitrogen.com/site/us/en/home/brands/ambion.html?CID=fl-ambion

Gene information for gene 351 (APP)

Gene:
Alternate gene names:CTFgamma, ABPP, PN2, PN-II, AAA, CVAP, APPI, ABETA, AD1
Description:amyloid beta (A4) precursor protein
Chromosome:21
Start:27252860
Stop:27543445
Strand:negative
Locus:21q21.3
Biotype:protein-coding
Status:live
Entrez Gene:
GeneCards:
Ensembl:
Hgnc:
Hprd:
Mim:
Uniprot:
Vega:
RefSeq:

Genome browser for gene 351 (APP)

Homo sapiens GRCh37
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